Multiple sequence alignment - TraesCS1B01G156000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G156000 chr1B 100.000 3275 0 0 1 3275 263744547 263747821 0.000000e+00 6048.0
1 TraesCS1B01G156000 chr1D 94.679 1090 49 7 1705 2793 189883304 189884385 0.000000e+00 1683.0
2 TraesCS1B01G156000 chr1D 94.683 884 23 4 828 1705 189882075 189882940 0.000000e+00 1351.0
3 TraesCS1B01G156000 chr1D 91.741 557 35 4 1 548 189799226 189799780 0.000000e+00 763.0
4 TraesCS1B01G156000 chr1D 95.406 283 11 2 2858 3139 189884384 189884665 1.790000e-122 449.0
5 TraesCS1B01G156000 chr1D 85.271 258 14 9 546 798 189801875 189802113 9.080000e-61 244.0
6 TraesCS1B01G156000 chr1D 95.556 135 4 2 3141 3275 189884629 189884761 7.120000e-52 215.0
7 TraesCS1B01G156000 chr1A 93.704 1096 59 7 1704 2793 167803759 167802668 0.000000e+00 1633.0
8 TraesCS1B01G156000 chr1A 95.165 786 30 1 920 1705 167804874 167804097 0.000000e+00 1234.0
9 TraesCS1B01G156000 chr1A 90.034 291 18 5 2858 3139 167802669 167802381 1.860000e-97 366.0
10 TraesCS1B01G156000 chr1A 93.233 133 6 2 3144 3275 167802415 167802285 3.330000e-45 193.0
11 TraesCS1B01G156000 chr1A 80.711 197 25 8 2207 2403 94836069 94836252 1.230000e-29 141.0
12 TraesCS1B01G156000 chr3D 88.506 87 6 4 2786 2871 355882358 355882441 5.780000e-18 102.0
13 TraesCS1B01G156000 chr6B 87.356 87 7 4 2792 2877 690750956 690750873 2.690000e-16 97.1
14 TraesCS1B01G156000 chr6B 86.364 88 8 4 2791 2877 229680947 229680863 3.480000e-15 93.5
15 TraesCS1B01G156000 chr5D 86.022 93 9 4 2790 2881 557506392 557506303 2.690000e-16 97.1
16 TraesCS1B01G156000 chr5B 88.095 84 6 4 2789 2871 706458120 706458200 2.690000e-16 97.1
17 TraesCS1B01G156000 chr6D 86.517 89 8 4 2790 2877 81746932 81746847 9.670000e-16 95.3
18 TraesCS1B01G156000 chr3B 87.805 82 6 4 2791 2871 54754911 54754989 3.480000e-15 93.5
19 TraesCS1B01G156000 chr4B 86.207 87 8 4 2792 2877 618591759 618591676 1.250000e-14 91.6
20 TraesCS1B01G156000 chr4D 84.946 93 9 5 2788 2878 501060388 501060477 4.500000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G156000 chr1B 263744547 263747821 3274 False 6048.0 6048 100.000 1 3275 1 chr1B.!!$F1 3274
1 TraesCS1B01G156000 chr1D 189882075 189884761 2686 False 924.5 1683 95.081 828 3275 4 chr1D.!!$F2 2447
2 TraesCS1B01G156000 chr1D 189799226 189802113 2887 False 503.5 763 88.506 1 798 2 chr1D.!!$F1 797
3 TraesCS1B01G156000 chr1A 167802285 167804874 2589 True 856.5 1633 93.034 920 3275 4 chr1A.!!$R1 2355

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
610 2717 0.190069 TACGAGGGCCATCATAGGGT 59.810 55.0 19.0 9.12 0.00 4.34 F
822 2932 0.246635 ATCCAGACAACGAGGAACCG 59.753 55.0 0.0 0.00 34.62 4.44 F
976 3086 0.323451 GCGAAGAAACCCCAATCCCT 60.323 55.0 0.0 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1675 3791 0.179070 TGTGCGCAGAGTTACCAACA 60.179 50.000 12.22 0.0 0.00 3.33 R
2146 4635 1.002888 CCTCATCTTGTCAGCCACAGT 59.997 52.381 0.00 0.0 35.97 3.55 R
2694 5187 1.330521 CAGACCAAACAACTGTGTCCG 59.669 52.381 0.00 0.0 36.80 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.919168 CCGCAATGGCATAGATAACATTTG 59.081 41.667 0.00 0.00 41.24 2.32
43 44 6.613699 TGGCATAGATAACATTTGGAAGGAT 58.386 36.000 0.00 0.00 0.00 3.24
44 45 7.754624 TGGCATAGATAACATTTGGAAGGATA 58.245 34.615 0.00 0.00 0.00 2.59
55 56 8.230848 ACATTTGGAAGGATACCCATGATATA 57.769 34.615 0.00 0.00 33.88 0.86
110 119 4.516698 GGTGAGCATATGGTAGATGGTTTG 59.483 45.833 7.54 0.00 35.24 2.93
169 178 5.755861 GCCCTATGTAGTCATGAACTTTCTC 59.244 44.000 0.00 0.00 39.55 2.87
171 180 5.980116 CCTATGTAGTCATGAACTTTCTCGG 59.020 44.000 0.00 0.00 39.55 4.63
179 188 1.702957 TGAACTTTCTCGGGGTCCATT 59.297 47.619 0.00 0.00 0.00 3.16
213 222 5.941948 TGCTTCAAGAGATACGATATCGA 57.058 39.130 30.75 14.91 43.02 3.59
224 233 2.482864 ACGATATCGATGCAATGCACA 58.517 42.857 30.75 0.00 41.61 4.57
233 242 3.504863 GATGCAATGCACACGAATTTCT 58.495 40.909 11.23 0.00 43.04 2.52
236 245 4.118410 TGCAATGCACACGAATTTCTTTT 58.882 34.783 2.72 0.00 31.71 2.27
252 261 9.411801 GAATTTCTTTTCCAGTATTCTTGAACC 57.588 33.333 0.00 0.00 0.00 3.62
253 262 6.554334 TTCTTTTCCAGTATTCTTGAACCG 57.446 37.500 0.00 0.00 0.00 4.44
296 306 6.456449 GCAAAAATTCATAGCAGAGCATTTGG 60.456 38.462 0.00 0.00 0.00 3.28
300 310 3.954200 TCATAGCAGAGCATTTGGTTCA 58.046 40.909 0.00 0.00 0.00 3.18
311 321 3.371898 GCATTTGGTTCATTGCCTTTAGC 59.628 43.478 0.00 0.00 44.14 3.09
317 327 3.950395 GGTTCATTGCCTTTAGCTCATCT 59.050 43.478 0.00 0.00 44.23 2.90
367 377 4.769488 GCCTCATATCCAGAGATGTACAGA 59.231 45.833 0.33 0.00 35.09 3.41
368 378 5.244851 GCCTCATATCCAGAGATGTACAGAA 59.755 44.000 0.33 0.00 35.09 3.02
372 382 6.784473 TCATATCCAGAGATGTACAGAATGGT 59.216 38.462 15.04 8.30 35.29 3.55
427 437 6.248433 AGGATGCCAGAACTCAAAATCTTTA 58.752 36.000 0.00 0.00 0.00 1.85
462 472 6.045318 GTCATCGAGATCTTGAAGAATTGGA 58.955 40.000 17.44 0.00 0.00 3.53
495 505 6.588348 TTGAGACTACGCATCAAATGTATG 57.412 37.500 0.00 0.00 30.33 2.39
504 514 5.402568 ACGCATCAAATGTATGTCGAGATAC 59.597 40.000 22.29 22.29 32.24 2.24
566 2673 5.518847 GTGTAATAGATAGCTTGTTCACGCA 59.481 40.000 0.00 0.00 0.00 5.24
571 2678 2.177394 TAGCTTGTTCACGCATCCAA 57.823 45.000 0.00 0.00 0.00 3.53
589 2696 0.321122 AAAAGCGGCCTGACTCAGAG 60.321 55.000 7.69 0.00 32.44 3.35
610 2717 0.190069 TACGAGGGCCATCATAGGGT 59.810 55.000 19.00 9.12 0.00 4.34
654 2761 1.878522 GCATCCACACCGCTACGAG 60.879 63.158 0.00 0.00 0.00 4.18
660 2767 1.470979 CCACACCGCTACGAGCTTAAT 60.471 52.381 0.00 0.00 39.60 1.40
661 2768 2.223641 CCACACCGCTACGAGCTTAATA 60.224 50.000 0.00 0.00 39.60 0.98
680 2787 5.945775 AATAAGCTACGAGTTTAACGAGC 57.054 39.130 0.00 6.33 35.72 5.03
681 2788 2.274920 AGCTACGAGTTTAACGAGCC 57.725 50.000 9.47 0.00 35.92 4.70
682 2789 1.542915 AGCTACGAGTTTAACGAGCCA 59.457 47.619 9.47 0.00 35.92 4.75
683 2790 2.029649 AGCTACGAGTTTAACGAGCCAA 60.030 45.455 9.47 0.00 35.92 4.52
684 2791 2.733026 GCTACGAGTTTAACGAGCCAAA 59.267 45.455 0.00 0.00 32.46 3.28
685 2792 3.422732 GCTACGAGTTTAACGAGCCAAAC 60.423 47.826 0.00 0.00 35.36 2.93
686 2793 1.523934 ACGAGTTTAACGAGCCAAACG 59.476 47.619 0.00 0.00 39.18 3.60
706 2813 2.464865 GATCGAGTGCTCATTACGCTT 58.535 47.619 0.00 0.00 0.00 4.68
742 2851 3.629058 TCGAAATAGAGAGTGCGTATGC 58.371 45.455 0.00 0.00 43.20 3.14
766 2876 8.138712 TGCACATTTATACGATGAGTGTATGTA 58.861 33.333 0.00 0.00 34.51 2.29
798 2908 5.907391 GTGAGCGTATGCAATTGTAAATACC 59.093 40.000 10.11 7.52 46.23 2.73
799 2909 5.008217 TGAGCGTATGCAATTGTAAATACCC 59.992 40.000 10.11 6.09 46.23 3.69
800 2910 4.884744 AGCGTATGCAATTGTAAATACCCA 59.115 37.500 10.11 0.00 46.23 4.51
801 2911 5.534654 AGCGTATGCAATTGTAAATACCCAT 59.465 36.000 10.11 2.06 46.23 4.00
802 2912 6.040391 AGCGTATGCAATTGTAAATACCCATT 59.960 34.615 10.11 0.00 46.23 3.16
803 2913 7.229707 AGCGTATGCAATTGTAAATACCCATTA 59.770 33.333 10.11 0.00 46.23 1.90
804 2914 8.026607 GCGTATGCAATTGTAAATACCCATTAT 58.973 33.333 7.40 0.00 42.15 1.28
805 2915 9.554724 CGTATGCAATTGTAAATACCCATTATC 57.445 33.333 7.40 0.00 0.00 1.75
806 2916 9.855021 GTATGCAATTGTAAATACCCATTATCC 57.145 33.333 7.40 0.00 0.00 2.59
807 2917 7.904558 TGCAATTGTAAATACCCATTATCCA 57.095 32.000 7.40 0.00 0.00 3.41
808 2918 7.950512 TGCAATTGTAAATACCCATTATCCAG 58.049 34.615 7.40 0.00 0.00 3.86
809 2919 7.782168 TGCAATTGTAAATACCCATTATCCAGA 59.218 33.333 7.40 0.00 0.00 3.86
810 2920 8.082242 GCAATTGTAAATACCCATTATCCAGAC 58.918 37.037 7.40 0.00 0.00 3.51
811 2921 9.130661 CAATTGTAAATACCCATTATCCAGACA 57.869 33.333 0.00 0.00 0.00 3.41
812 2922 9.707957 AATTGTAAATACCCATTATCCAGACAA 57.292 29.630 0.00 0.00 0.00 3.18
813 2923 8.514330 TTGTAAATACCCATTATCCAGACAAC 57.486 34.615 0.00 0.00 0.00 3.32
814 2924 6.764085 TGTAAATACCCATTATCCAGACAACG 59.236 38.462 0.00 0.00 0.00 4.10
815 2925 5.623956 AATACCCATTATCCAGACAACGA 57.376 39.130 0.00 0.00 0.00 3.85
816 2926 3.543680 ACCCATTATCCAGACAACGAG 57.456 47.619 0.00 0.00 0.00 4.18
817 2927 2.170607 ACCCATTATCCAGACAACGAGG 59.829 50.000 0.00 0.00 0.00 4.63
818 2928 2.434336 CCCATTATCCAGACAACGAGGA 59.566 50.000 0.00 0.00 35.59 3.71
819 2929 3.118408 CCCATTATCCAGACAACGAGGAA 60.118 47.826 0.00 0.00 34.62 3.36
820 2930 3.871594 CCATTATCCAGACAACGAGGAAC 59.128 47.826 0.00 0.00 34.62 3.62
821 2931 3.604875 TTATCCAGACAACGAGGAACC 57.395 47.619 0.00 0.00 34.62 3.62
822 2932 0.246635 ATCCAGACAACGAGGAACCG 59.753 55.000 0.00 0.00 34.62 4.44
823 2933 1.111116 TCCAGACAACGAGGAACCGT 61.111 55.000 0.00 0.00 45.64 4.83
889 2999 4.752879 ACCCCACGCATCGGTTCG 62.753 66.667 0.00 0.00 0.00 3.95
976 3086 0.323451 GCGAAGAAACCCCAATCCCT 60.323 55.000 0.00 0.00 0.00 4.20
1047 3157 3.393970 CGCCCTCTCTTCCAGCCA 61.394 66.667 0.00 0.00 0.00 4.75
1050 3160 1.557269 GCCCTCTCTTCCAGCCAGAA 61.557 60.000 0.00 0.00 0.00 3.02
1057 3167 1.294659 CTTCCAGCCAGAAGACGTGC 61.295 60.000 7.41 0.00 45.08 5.34
1422 3538 1.749638 CGTCGAGCTCACCCCTACT 60.750 63.158 15.40 0.00 0.00 2.57
1604 3720 4.394795 CCAAGTAAGAAAACGCGATGAAG 58.605 43.478 15.93 0.00 0.00 3.02
1675 3791 8.814038 ATATGTGCAAATAGAAGGAAAGTTCT 57.186 30.769 2.42 0.00 40.07 3.01
1678 3794 6.321181 TGTGCAAATAGAAGGAAAGTTCTGTT 59.679 34.615 0.00 0.00 38.96 3.16
1686 3802 6.056236 AGAAGGAAAGTTCTGTTGGTAACTC 58.944 40.000 0.00 0.00 35.37 3.01
1705 3821 1.737236 TCTGCGCACAATGTGGAATAC 59.263 47.619 15.78 0.00 33.64 1.89
1706 3822 1.468127 CTGCGCACAATGTGGAATACA 59.532 47.619 15.78 0.00 44.87 2.29
1717 4199 3.616219 TGTGGAATACAACCTATGTGCC 58.384 45.455 0.00 0.00 43.77 5.01
1792 4274 6.947158 TGGCCATGATGCAAATTATAGATGTA 59.053 34.615 0.00 0.00 0.00 2.29
1816 4298 2.972625 TGTTGGAAGGAGCGTCAATAG 58.027 47.619 0.00 0.00 0.00 1.73
1851 4333 9.878599 AGAGTTTAATGAATTTGACAAACTACG 57.121 29.630 1.94 0.00 36.60 3.51
1931 4413 2.110188 AGATAGAGGGAACGGGCATAGA 59.890 50.000 0.00 0.00 0.00 1.98
1933 4415 1.807814 AGAGGGAACGGGCATAGAAT 58.192 50.000 0.00 0.00 0.00 2.40
1988 4471 3.504863 GCACAGTGCAGTGATTTAATGG 58.495 45.455 28.02 7.49 44.26 3.16
2016 4505 5.759506 TTGTGTGTGGTGGTTAATTGTAG 57.240 39.130 0.00 0.00 0.00 2.74
2281 4770 4.336280 GGCCTTTGAGGACTAAAAGATGT 58.664 43.478 10.18 0.00 41.45 3.06
2339 4828 5.051816 TGGTTTCAAGTACAAGTCCTTACG 58.948 41.667 0.00 0.00 0.00 3.18
2364 4853 4.310769 CAGTTCTGTTCCAAGTAGTCTGG 58.689 47.826 0.00 0.00 0.00 3.86
2371 4860 7.179966 TCTGTTCCAAGTAGTCTGGTAGATAA 58.820 38.462 0.00 0.00 0.00 1.75
2393 4886 4.862902 ATAGATGGATGAGTCGGTGAAG 57.137 45.455 0.00 0.00 0.00 3.02
2403 4896 3.118920 TGAGTCGGTGAAGACAGAAAACA 60.119 43.478 0.00 0.00 43.24 2.83
2419 4912 3.678056 AAACAGAGAAGCACCGTATGA 57.322 42.857 0.00 0.00 0.00 2.15
2426 4919 4.463186 AGAGAAGCACCGTATGAGTTAGTT 59.537 41.667 0.00 0.00 0.00 2.24
2427 4920 5.651139 AGAGAAGCACCGTATGAGTTAGTTA 59.349 40.000 0.00 0.00 0.00 2.24
2503 4996 3.057806 GGTTTCGAAATGGTTGAATCGGT 60.058 43.478 14.69 0.00 36.05 4.69
2515 5008 7.185318 TGGTTGAATCGGTAGAACCTTAATA 57.815 36.000 9.53 0.00 38.96 0.98
2650 5143 1.871080 CCACGCTTGGCCTTATCTAG 58.129 55.000 3.32 0.00 35.56 2.43
2789 5282 9.392259 GACTAGGGTACAAATTAAGCTTGTAAT 57.608 33.333 9.86 0.00 40.11 1.89
2801 5294 9.915629 AATTAAGCTTGTAATATACTCTCTCCG 57.084 33.333 9.86 0.00 0.00 4.63
2802 5295 6.963083 AAGCTTGTAATATACTCTCTCCGT 57.037 37.500 0.00 0.00 0.00 4.69
2803 5296 6.963083 AGCTTGTAATATACTCTCTCCGTT 57.037 37.500 0.00 0.00 0.00 4.44
2804 5297 6.972722 AGCTTGTAATATACTCTCTCCGTTC 58.027 40.000 0.00 0.00 0.00 3.95
2805 5298 6.016108 AGCTTGTAATATACTCTCTCCGTTCC 60.016 42.308 0.00 0.00 0.00 3.62
2806 5299 6.016108 GCTTGTAATATACTCTCTCCGTTCCT 60.016 42.308 0.00 0.00 0.00 3.36
2807 5300 7.174599 GCTTGTAATATACTCTCTCCGTTCCTA 59.825 40.741 0.00 0.00 0.00 2.94
2808 5301 8.985315 TTGTAATATACTCTCTCCGTTCCTAA 57.015 34.615 0.00 0.00 0.00 2.69
2809 5302 8.985315 TGTAATATACTCTCTCCGTTCCTAAA 57.015 34.615 0.00 0.00 0.00 1.85
2810 5303 9.584008 TGTAATATACTCTCTCCGTTCCTAAAT 57.416 33.333 0.00 0.00 0.00 1.40
2816 5309 9.810870 ATACTCTCTCCGTTCCTAAATATAAGT 57.189 33.333 0.00 0.00 0.00 2.24
2817 5310 8.536340 ACTCTCTCCGTTCCTAAATATAAGTT 57.464 34.615 0.00 0.00 0.00 2.66
2818 5311 8.979534 ACTCTCTCCGTTCCTAAATATAAGTTT 58.020 33.333 0.00 0.00 0.00 2.66
2819 5312 9.819267 CTCTCTCCGTTCCTAAATATAAGTTTT 57.181 33.333 0.00 0.00 0.00 2.43
2849 5342 7.877003 AGAGATTCCACTATGAACTACATACG 58.123 38.462 0.00 0.00 40.07 3.06
2850 5343 6.982852 AGATTCCACTATGAACTACATACGG 58.017 40.000 0.00 0.00 40.07 4.02
2851 5344 6.776116 AGATTCCACTATGAACTACATACGGA 59.224 38.462 0.00 0.00 40.07 4.69
2852 5345 6.387041 TTCCACTATGAACTACATACGGAG 57.613 41.667 0.00 0.00 38.29 4.63
2853 5346 4.825634 TCCACTATGAACTACATACGGAGG 59.174 45.833 0.00 0.00 40.07 4.30
2854 5347 4.825634 CCACTATGAACTACATACGGAGGA 59.174 45.833 0.00 0.00 40.07 3.71
2855 5348 5.477291 CCACTATGAACTACATACGGAGGAT 59.523 44.000 0.00 0.00 40.07 3.24
2856 5349 6.015350 CCACTATGAACTACATACGGAGGATT 60.015 42.308 0.00 0.00 40.07 3.01
2956 5451 5.477291 TGGGGAAAATGCAGTATTTACGAAA 59.523 36.000 0.00 0.00 38.01 3.46
3091 5593 9.241919 TCATATTAATATATGGTTGTTGCCTGG 57.758 33.333 7.65 0.00 42.53 4.45
3102 5604 1.133199 TGTTGCCTGGGAAGGACATTT 60.133 47.619 0.00 0.00 0.00 2.32
3103 5605 1.546029 GTTGCCTGGGAAGGACATTTC 59.454 52.381 0.00 0.00 0.00 2.17
3104 5606 0.039618 TGCCTGGGAAGGACATTTCC 59.960 55.000 0.00 0.00 44.82 3.13
3116 5618 3.642705 GGACATTTCCTGTTCAACTTGC 58.357 45.455 0.00 0.00 38.54 4.01
3117 5619 3.068024 GGACATTTCCTGTTCAACTTGCA 59.932 43.478 0.00 0.00 38.54 4.08
3118 5620 4.441356 GGACATTTCCTGTTCAACTTGCAA 60.441 41.667 0.00 0.00 38.54 4.08
3119 5621 4.685924 ACATTTCCTGTTCAACTTGCAAG 58.314 39.130 24.84 24.84 32.90 4.01
3120 5622 4.402155 ACATTTCCTGTTCAACTTGCAAGA 59.598 37.500 32.50 8.21 32.90 3.02
3121 5623 4.637483 TTTCCTGTTCAACTTGCAAGAG 57.363 40.909 32.50 22.46 0.00 2.85
3122 5624 3.558931 TCCTGTTCAACTTGCAAGAGA 57.441 42.857 32.50 24.22 0.00 3.10
3123 5625 4.090761 TCCTGTTCAACTTGCAAGAGAT 57.909 40.909 32.50 15.00 0.00 2.75
3124 5626 3.817084 TCCTGTTCAACTTGCAAGAGATG 59.183 43.478 32.50 24.38 0.00 2.90
3140 5642 7.187244 CAAGAGATGCATCGAAGATAAATGT 57.813 36.000 20.67 0.00 45.12 2.71
3160 5663 2.291741 GTCCTGTTCAACTTGCAAGAGG 59.708 50.000 32.50 24.83 34.92 3.69
3203 5706 7.824289 CAGGTACTAACATCTTTCCATTCTGAA 59.176 37.037 0.00 0.00 36.02 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 6.088016 TCCAAATGTTATCTATGCCATTGC 57.912 37.500 0.00 0.00 38.26 3.56
22 23 8.163408 TGGGTATCCTTCCAAATGTTATCTATG 58.837 37.037 0.00 0.00 0.00 2.23
23 24 8.287904 TGGGTATCCTTCCAAATGTTATCTAT 57.712 34.615 0.00 0.00 0.00 1.98
36 37 4.721776 TGGCTATATCATGGGTATCCTTCC 59.278 45.833 0.00 0.00 0.00 3.46
43 44 5.966319 ACTGATGATGGCTATATCATGGGTA 59.034 40.000 13.65 0.00 45.30 3.69
44 45 4.786994 ACTGATGATGGCTATATCATGGGT 59.213 41.667 13.65 10.01 45.30 4.51
55 56 1.496429 CCCCCTTAACTGATGATGGCT 59.504 52.381 0.00 0.00 0.00 4.75
110 119 4.201647 CCGAGCATTTGACATTTGCAAATC 60.202 41.667 21.70 13.28 42.33 2.17
138 147 3.931747 ATGACTACATAGGGCCTTCGCC 61.932 54.545 13.45 0.00 44.04 5.54
139 148 0.750850 TGACTACATAGGGCCTTCGC 59.249 55.000 13.45 0.00 0.00 4.70
142 151 4.040755 AGTTCATGACTACATAGGGCCTT 58.959 43.478 13.45 0.00 36.65 4.35
169 178 2.398554 CGCTTCACAATGGACCCCG 61.399 63.158 0.00 0.00 0.00 5.73
171 180 1.243902 TTTCGCTTCACAATGGACCC 58.756 50.000 0.00 0.00 0.00 4.46
198 207 5.039984 GCATTGCATCGATATCGTATCTCT 58.960 41.667 23.61 4.83 40.80 3.10
213 222 3.581024 AGAAATTCGTGTGCATTGCAT 57.419 38.095 15.49 0.00 41.91 3.96
224 233 8.391075 TCAAGAATACTGGAAAAGAAATTCGT 57.609 30.769 0.00 0.00 37.13 3.85
233 242 4.076394 CCCGGTTCAAGAATACTGGAAAA 58.924 43.478 0.00 0.00 42.32 2.29
236 245 1.557832 CCCCGGTTCAAGAATACTGGA 59.442 52.381 0.00 0.00 42.32 3.86
252 261 2.230992 TGCATCACTTCAATTTTCCCCG 59.769 45.455 0.00 0.00 0.00 5.73
253 262 3.959535 TGCATCACTTCAATTTTCCCC 57.040 42.857 0.00 0.00 0.00 4.81
296 306 6.874288 ATAGATGAGCTAAAGGCAATGAAC 57.126 37.500 0.00 0.00 44.79 3.18
300 310 5.945310 TGGAATAGATGAGCTAAAGGCAAT 58.055 37.500 0.00 0.00 44.79 3.56
342 352 2.981921 ACATCTCTGGATATGAGGCCA 58.018 47.619 5.01 0.00 32.78 5.36
368 378 9.699410 TGAGTCCATTCTTCAATTTTATACCAT 57.301 29.630 0.00 0.00 0.00 3.55
372 382 9.613428 ATCGTGAGTCCATTCTTCAATTTTATA 57.387 29.630 0.00 0.00 0.00 0.98
462 472 4.002982 TGCGTAGTCTCAAATGCTTTCAT 58.997 39.130 0.00 0.00 33.53 2.57
495 505 6.621164 GGATATTTCCTCACGAGTATCTCGAC 60.621 46.154 22.76 0.00 46.09 4.20
504 514 4.022762 AGTCATCGGATATTTCCTCACGAG 60.023 45.833 0.46 0.00 40.17 4.18
507 517 4.950050 ACAGTCATCGGATATTTCCTCAC 58.050 43.478 0.46 0.00 40.17 3.51
530 540 4.895224 TCTATTACACTAGTGCTCCACG 57.105 45.455 22.90 7.46 39.64 4.94
531 541 6.207810 AGCTATCTATTACACTAGTGCTCCAC 59.792 42.308 22.90 2.67 34.10 4.02
566 2673 0.678048 GAGTCAGGCCGCTTTTGGAT 60.678 55.000 0.00 0.00 0.00 3.41
571 2678 1.294780 CTCTGAGTCAGGCCGCTTT 59.705 57.895 19.99 0.00 31.51 3.51
579 2686 1.384525 CCCTCGTACCTCTGAGTCAG 58.615 60.000 14.36 14.36 0.00 3.51
589 2696 0.608640 CCTATGATGGCCCTCGTACC 59.391 60.000 5.90 0.00 0.00 3.34
628 2735 1.700523 CGGTGTGGATGCACAAAATG 58.299 50.000 22.48 8.17 40.89 2.32
629 2736 0.038343 GCGGTGTGGATGCACAAAAT 60.038 50.000 22.48 0.00 40.89 1.82
630 2737 1.106351 AGCGGTGTGGATGCACAAAA 61.106 50.000 22.48 0.00 40.89 2.44
631 2738 0.250510 TAGCGGTGTGGATGCACAAA 60.251 50.000 22.48 0.00 40.89 2.83
638 2745 2.494918 GCTCGTAGCGGTGTGGAT 59.505 61.111 0.00 0.00 0.00 3.41
660 2767 3.191162 TGGCTCGTTAAACTCGTAGCTTA 59.809 43.478 0.00 0.00 34.56 3.09
661 2768 2.029649 TGGCTCGTTAAACTCGTAGCTT 60.030 45.455 0.00 0.00 34.56 3.74
665 2772 2.725723 CGTTTGGCTCGTTAAACTCGTA 59.274 45.455 0.00 0.00 35.26 3.43
667 2774 1.788308 TCGTTTGGCTCGTTAAACTCG 59.212 47.619 0.00 0.00 35.26 4.18
668 2775 3.481467 CGATCGTTTGGCTCGTTAAACTC 60.481 47.826 7.03 0.00 35.26 3.01
669 2776 2.410730 CGATCGTTTGGCTCGTTAAACT 59.589 45.455 7.03 0.00 35.26 2.66
670 2777 2.409378 TCGATCGTTTGGCTCGTTAAAC 59.591 45.455 15.94 0.00 34.19 2.01
671 2778 2.664568 CTCGATCGTTTGGCTCGTTAAA 59.335 45.455 15.94 0.00 34.19 1.52
672 2779 2.256174 CTCGATCGTTTGGCTCGTTAA 58.744 47.619 15.94 0.00 34.19 2.01
673 2780 1.200716 ACTCGATCGTTTGGCTCGTTA 59.799 47.619 15.94 0.00 34.19 3.18
674 2781 0.038526 ACTCGATCGTTTGGCTCGTT 60.039 50.000 15.94 0.00 34.19 3.85
675 2782 0.732880 CACTCGATCGTTTGGCTCGT 60.733 55.000 15.94 0.00 34.19 4.18
676 2783 1.991430 CACTCGATCGTTTGGCTCG 59.009 57.895 15.94 0.00 0.00 5.03
677 2784 0.737715 AGCACTCGATCGTTTGGCTC 60.738 55.000 15.94 1.54 0.00 4.70
678 2785 0.737715 GAGCACTCGATCGTTTGGCT 60.738 55.000 15.94 18.46 0.00 4.75
679 2786 1.014044 TGAGCACTCGATCGTTTGGC 61.014 55.000 15.94 14.23 0.00 4.52
680 2787 1.645034 ATGAGCACTCGATCGTTTGG 58.355 50.000 15.94 6.78 0.00 3.28
681 2788 3.301197 CGTAATGAGCACTCGATCGTTTG 60.301 47.826 15.94 13.91 37.85 2.93
682 2789 2.852413 CGTAATGAGCACTCGATCGTTT 59.148 45.455 15.94 0.00 37.85 3.60
683 2790 2.451132 CGTAATGAGCACTCGATCGTT 58.549 47.619 15.94 1.68 39.92 3.85
684 2791 1.860399 GCGTAATGAGCACTCGATCGT 60.860 52.381 15.94 0.00 34.19 3.73
685 2792 0.772926 GCGTAATGAGCACTCGATCG 59.227 55.000 9.36 9.36 34.19 3.69
686 2793 2.126914 AGCGTAATGAGCACTCGATC 57.873 50.000 0.00 0.00 37.01 3.69
706 2813 6.630071 TCTATTTCGATGAACACATCTCACA 58.370 36.000 0.00 0.00 38.46 3.58
752 2861 7.138736 TCACATACACATACATACACTCATCG 58.861 38.462 0.00 0.00 0.00 3.84
753 2862 7.115520 GCTCACATACACATACATACACTCATC 59.884 40.741 0.00 0.00 0.00 2.92
754 2863 6.925718 GCTCACATACACATACATACACTCAT 59.074 38.462 0.00 0.00 0.00 2.90
766 2876 3.177997 TGCATACGCTCACATACACAT 57.822 42.857 0.00 0.00 39.64 3.21
798 2908 3.819564 TCCTCGTTGTCTGGATAATGG 57.180 47.619 0.78 0.00 0.00 3.16
799 2909 3.871594 GGTTCCTCGTTGTCTGGATAATG 59.128 47.826 0.00 0.00 0.00 1.90
800 2910 3.430374 CGGTTCCTCGTTGTCTGGATAAT 60.430 47.826 0.00 0.00 0.00 1.28
801 2911 2.094390 CGGTTCCTCGTTGTCTGGATAA 60.094 50.000 0.00 0.00 0.00 1.75
802 2912 1.475280 CGGTTCCTCGTTGTCTGGATA 59.525 52.381 0.00 0.00 0.00 2.59
803 2913 0.246635 CGGTTCCTCGTTGTCTGGAT 59.753 55.000 0.00 0.00 0.00 3.41
804 2914 1.111116 ACGGTTCCTCGTTGTCTGGA 61.111 55.000 0.00 0.00 40.85 3.86
805 2915 1.366366 ACGGTTCCTCGTTGTCTGG 59.634 57.895 0.00 0.00 40.85 3.86
847 2957 0.877743 TCATGGCGCAATTCGTTTGA 59.122 45.000 10.83 0.00 41.07 2.69
889 2999 1.080705 CGAACCAGGTGTCCGACTC 60.081 63.158 0.00 0.00 0.00 3.36
976 3086 2.203773 GGGCTTTGGGGGCTTTGA 60.204 61.111 0.00 0.00 0.00 2.69
1110 3226 2.304221 TCACCTCCTCCGAAGAAGAA 57.696 50.000 0.00 0.00 0.00 2.52
1147 3263 0.901124 TTCTCCTCCTGCTTCTCTGC 59.099 55.000 0.00 0.00 0.00 4.26
1422 3538 1.617018 CGGGCTTGATGGAGGAGACA 61.617 60.000 0.00 0.00 0.00 3.41
1675 3791 0.179070 TGTGCGCAGAGTTACCAACA 60.179 50.000 12.22 0.00 0.00 3.33
1678 3794 1.155889 CATTGTGCGCAGAGTTACCA 58.844 50.000 12.22 0.00 0.00 3.25
1686 3802 1.468127 TGTATTCCACATTGTGCGCAG 59.532 47.619 12.22 0.12 30.04 5.18
1705 3821 5.125356 TCACATCATAAGGCACATAGGTTG 58.875 41.667 0.00 0.00 0.00 3.77
1706 3822 5.130975 TCTCACATCATAAGGCACATAGGTT 59.869 40.000 0.00 0.00 0.00 3.50
1717 4199 7.380870 CGGTAGTTCTGATTCTCACATCATAAG 59.619 40.741 0.00 0.00 32.59 1.73
1742 4224 4.124238 ACGTTCCATACATTATGTTCCCG 58.876 43.478 2.23 1.22 34.36 5.14
1792 4274 2.582052 TGACGCTCCTTCCAACATTTT 58.418 42.857 0.00 0.00 0.00 1.82
1816 4298 9.528018 TCAAATTCATTAAACTCTTTGGACAAC 57.472 29.630 0.00 0.00 0.00 3.32
1904 4386 3.358118 CCCGTTCCCTCTATCTATCTCC 58.642 54.545 0.00 0.00 0.00 3.71
1931 4413 4.937620 ACAAATCGCTGACACATAGACATT 59.062 37.500 0.00 0.00 0.00 2.71
1933 4415 3.925379 ACAAATCGCTGACACATAGACA 58.075 40.909 0.00 0.00 0.00 3.41
1947 4430 7.003939 TGTGCACATTAGATCTAACAAATCG 57.996 36.000 17.42 4.89 0.00 3.34
2016 4505 4.320935 CCACACTAGTTATTTTGCCACCAC 60.321 45.833 0.00 0.00 0.00 4.16
2146 4635 1.002888 CCTCATCTTGTCAGCCACAGT 59.997 52.381 0.00 0.00 35.97 3.55
2235 4724 1.673329 GCGTTCTCCTTCCTGACTTCC 60.673 57.143 0.00 0.00 0.00 3.46
2281 4770 3.476552 AGACAAAAGCAAGATCAACCGA 58.523 40.909 0.00 0.00 0.00 4.69
2339 4828 4.039366 AGACTACTTGGAACAGAACTGGAC 59.961 45.833 6.76 0.38 42.39 4.02
2364 4853 7.971168 CACCGACTCATCCATCTATTTATCTAC 59.029 40.741 0.00 0.00 0.00 2.59
2371 4860 4.895889 TCTTCACCGACTCATCCATCTATT 59.104 41.667 0.00 0.00 0.00 1.73
2393 4886 2.221981 CGGTGCTTCTCTGTTTTCTGTC 59.778 50.000 0.00 0.00 0.00 3.51
2403 4896 4.017808 ACTAACTCATACGGTGCTTCTCT 58.982 43.478 0.00 0.00 0.00 3.10
2427 4920 9.698309 CAAAACTCTCCTGTATACGATGATTAT 57.302 33.333 0.00 0.00 0.00 1.28
2503 4996 6.368779 ACACAGGTTGCTATTAAGGTTCTA 57.631 37.500 0.00 0.00 0.00 2.10
2515 5008 5.852282 AACTTAATTGAACACAGGTTGCT 57.148 34.783 0.00 0.00 37.36 3.91
2634 5127 2.103263 AGTTCCTAGATAAGGCCAAGCG 59.897 50.000 5.01 0.00 46.10 4.68
2650 5143 3.081804 CAACATACAGGTTCCCAGTTCC 58.918 50.000 0.00 0.00 0.00 3.62
2654 5147 4.000988 GTGTACAACATACAGGTTCCCAG 58.999 47.826 0.00 0.00 0.00 4.45
2694 5187 1.330521 CAGACCAAACAACTGTGTCCG 59.669 52.381 0.00 0.00 36.80 4.79
2791 5284 9.638176 AACTTATATTTAGGAACGGAGAGAGTA 57.362 33.333 0.00 0.00 0.00 2.59
2792 5285 8.536340 AACTTATATTTAGGAACGGAGAGAGT 57.464 34.615 0.00 0.00 0.00 3.24
2793 5286 9.819267 AAAACTTATATTTAGGAACGGAGAGAG 57.181 33.333 0.00 0.00 0.00 3.20
2823 5316 9.000486 CGTATGTAGTTCATAGTGGAATCTCTA 58.000 37.037 0.00 0.00 39.36 2.43
2824 5317 7.040340 CCGTATGTAGTTCATAGTGGAATCTCT 60.040 40.741 3.20 0.00 39.36 3.10
2825 5318 7.040617 TCCGTATGTAGTTCATAGTGGAATCTC 60.041 40.741 7.73 0.00 39.60 2.75
2826 5319 6.776116 TCCGTATGTAGTTCATAGTGGAATCT 59.224 38.462 7.73 0.00 39.60 2.40
2827 5320 6.978338 TCCGTATGTAGTTCATAGTGGAATC 58.022 40.000 7.73 0.00 39.60 2.52
2828 5321 6.015350 CCTCCGTATGTAGTTCATAGTGGAAT 60.015 42.308 10.20 0.00 40.80 3.01
2829 5322 5.301045 CCTCCGTATGTAGTTCATAGTGGAA 59.699 44.000 10.20 0.00 40.80 3.53
2830 5323 4.825634 CCTCCGTATGTAGTTCATAGTGGA 59.174 45.833 9.16 9.16 39.94 4.02
2831 5324 4.825634 TCCTCCGTATGTAGTTCATAGTGG 59.174 45.833 2.99 2.99 39.36 4.00
2832 5325 6.576662 ATCCTCCGTATGTAGTTCATAGTG 57.423 41.667 0.00 0.00 39.36 2.74
2833 5326 7.598759 AAATCCTCCGTATGTAGTTCATAGT 57.401 36.000 0.00 0.00 39.36 2.12
2834 5327 9.574458 CATAAATCCTCCGTATGTAGTTCATAG 57.426 37.037 0.00 0.00 39.36 2.23
2835 5328 8.033038 GCATAAATCCTCCGTATGTAGTTCATA 58.967 37.037 0.00 0.00 37.91 2.15
2836 5329 6.874134 GCATAAATCCTCCGTATGTAGTTCAT 59.126 38.462 0.00 0.00 40.25 2.57
2837 5330 6.041637 AGCATAAATCCTCCGTATGTAGTTCA 59.958 38.462 0.00 0.00 0.00 3.18
2838 5331 6.366332 CAGCATAAATCCTCCGTATGTAGTTC 59.634 42.308 0.00 0.00 0.00 3.01
2839 5332 6.223852 CAGCATAAATCCTCCGTATGTAGTT 58.776 40.000 0.00 0.00 0.00 2.24
2840 5333 5.784177 CAGCATAAATCCTCCGTATGTAGT 58.216 41.667 0.00 0.00 0.00 2.73
2841 5334 4.627467 GCAGCATAAATCCTCCGTATGTAG 59.373 45.833 0.00 0.00 0.00 2.74
2842 5335 4.039852 TGCAGCATAAATCCTCCGTATGTA 59.960 41.667 0.00 0.00 0.00 2.29
2843 5336 3.181455 TGCAGCATAAATCCTCCGTATGT 60.181 43.478 0.00 0.00 0.00 2.29
2844 5337 3.402110 TGCAGCATAAATCCTCCGTATG 58.598 45.455 0.00 0.00 0.00 2.39
2845 5338 3.769739 TGCAGCATAAATCCTCCGTAT 57.230 42.857 0.00 0.00 0.00 3.06
2846 5339 3.181455 ACATGCAGCATAAATCCTCCGTA 60.181 43.478 7.82 0.00 0.00 4.02
2847 5340 2.224606 CATGCAGCATAAATCCTCCGT 58.775 47.619 7.82 0.00 0.00 4.69
2848 5341 2.224606 ACATGCAGCATAAATCCTCCG 58.775 47.619 7.82 0.00 0.00 4.63
2849 5342 4.660789 AAACATGCAGCATAAATCCTCC 57.339 40.909 7.82 0.00 0.00 4.30
2850 5343 5.870978 ACAAAAACATGCAGCATAAATCCTC 59.129 36.000 7.82 0.00 0.00 3.71
2851 5344 5.640357 CACAAAAACATGCAGCATAAATCCT 59.360 36.000 7.82 0.00 0.00 3.24
2852 5345 5.409214 ACACAAAAACATGCAGCATAAATCC 59.591 36.000 7.82 0.00 0.00 3.01
2853 5346 6.470557 ACACAAAAACATGCAGCATAAATC 57.529 33.333 7.82 0.00 0.00 2.17
2854 5347 7.959689 TTACACAAAAACATGCAGCATAAAT 57.040 28.000 7.82 0.00 0.00 1.40
2855 5348 7.776933 TTTACACAAAAACATGCAGCATAAA 57.223 28.000 7.82 0.00 0.00 1.40
2856 5349 7.440556 ACATTTACACAAAAACATGCAGCATAA 59.559 29.630 7.82 0.00 0.00 1.90
2932 5427 4.590918 TCGTAAATACTGCATTTTCCCCA 58.409 39.130 0.00 0.00 37.93 4.96
2956 5451 6.546428 ACACTATACAAGCACCAAGTCTAT 57.454 37.500 0.00 0.00 0.00 1.98
2991 5486 5.118286 CAAGTTTCAAATGGCCAGAACTTT 58.882 37.500 21.40 12.03 0.00 2.66
2997 5493 4.599047 TTACCAAGTTTCAAATGGCCAG 57.401 40.909 13.05 0.00 37.77 4.85
3102 5604 3.558931 TCTCTTGCAAGTTGAACAGGA 57.441 42.857 25.19 9.37 0.00 3.86
3103 5605 4.156664 CATCTCTTGCAAGTTGAACAGG 57.843 45.455 25.19 12.02 0.00 4.00
3116 5618 7.187244 ACATTTATCTTCGATGCATCTCTTG 57.813 36.000 23.73 8.91 0.00 3.02
3117 5619 6.426328 GGACATTTATCTTCGATGCATCTCTT 59.574 38.462 23.73 7.31 0.00 2.85
3118 5620 5.931146 GGACATTTATCTTCGATGCATCTCT 59.069 40.000 23.73 6.82 0.00 3.10
3119 5621 5.931146 AGGACATTTATCTTCGATGCATCTC 59.069 40.000 23.73 9.90 0.00 2.75
3120 5622 5.699915 CAGGACATTTATCTTCGATGCATCT 59.300 40.000 23.73 7.83 0.00 2.90
3121 5623 5.468072 ACAGGACATTTATCTTCGATGCATC 59.532 40.000 17.10 17.10 0.00 3.91
3122 5624 5.371526 ACAGGACATTTATCTTCGATGCAT 58.628 37.500 0.00 0.00 0.00 3.96
3123 5625 4.769688 ACAGGACATTTATCTTCGATGCA 58.230 39.130 0.00 0.00 0.00 3.96
3124 5626 5.294306 TGAACAGGACATTTATCTTCGATGC 59.706 40.000 0.00 0.00 0.00 3.91
3125 5627 6.908870 TGAACAGGACATTTATCTTCGATG 57.091 37.500 0.00 0.00 0.00 3.84
3126 5628 7.106239 AGTTGAACAGGACATTTATCTTCGAT 58.894 34.615 0.00 0.00 0.00 3.59
3127 5629 6.464222 AGTTGAACAGGACATTTATCTTCGA 58.536 36.000 0.00 0.00 0.00 3.71
3128 5630 6.727824 AGTTGAACAGGACATTTATCTTCG 57.272 37.500 0.00 0.00 0.00 3.79
3129 5631 6.803807 GCAAGTTGAACAGGACATTTATCTTC 59.196 38.462 7.16 0.00 0.00 2.87
3130 5632 6.265196 TGCAAGTTGAACAGGACATTTATCTT 59.735 34.615 7.16 0.00 0.00 2.40
3131 5633 5.769662 TGCAAGTTGAACAGGACATTTATCT 59.230 36.000 7.16 0.00 0.00 1.98
3132 5634 6.012658 TGCAAGTTGAACAGGACATTTATC 57.987 37.500 7.16 0.00 0.00 1.75
3133 5635 6.265196 TCTTGCAAGTTGAACAGGACATTTAT 59.735 34.615 25.19 0.00 0.00 1.40
3134 5636 5.592282 TCTTGCAAGTTGAACAGGACATTTA 59.408 36.000 25.19 0.00 0.00 1.40
3135 5637 4.402155 TCTTGCAAGTTGAACAGGACATTT 59.598 37.500 25.19 0.00 0.00 2.32
3136 5638 3.953612 TCTTGCAAGTTGAACAGGACATT 59.046 39.130 25.19 0.00 0.00 2.71
3137 5639 3.554934 TCTTGCAAGTTGAACAGGACAT 58.445 40.909 25.19 0.00 0.00 3.06
3138 5640 2.945008 CTCTTGCAAGTTGAACAGGACA 59.055 45.455 25.19 1.23 0.00 4.02
3139 5641 2.291741 CCTCTTGCAAGTTGAACAGGAC 59.708 50.000 25.19 0.00 0.00 3.85
3140 5642 2.092429 ACCTCTTGCAAGTTGAACAGGA 60.092 45.455 27.49 7.63 0.00 3.86
3160 5663 9.982651 TTAGTACCTGATTTATCTTCTATGCAC 57.017 33.333 0.00 0.00 0.00 4.57
3222 5725 7.607615 ATGGAATTAGAAAGCTTAATGCCAT 57.392 32.000 20.75 20.75 41.67 4.40
3223 5726 7.093377 ACAATGGAATTAGAAAGCTTAATGCCA 60.093 33.333 18.58 18.58 41.65 4.92


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.